From 6813db912f61e394429afdf67d07661fc1897e24 Mon Sep 17 00:00:00 2001
From: Aditya Bijalwan <187593306+kunal-10-cloud@users.noreply.github.com>
Date: Wed, 15 Apr 2026 23:17:40 +0530
Subject: [PATCH 1/4] fix: expand coverage to full malariagen_data package and
 update codecov action

- Changed --cov target from malariagen_data/anoph to malariagen_data so
  coverage measurement includes all root-level modules (ag3.py, af1.py,
  plasmodium.py, veff.py, util.py, etc.) that were previously excluded
- Updated codecov/codecov-action from v3 to v4 for security fixes

Closes #1301
---
 .github/workflows/coverage.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
index f5c4f0248..0f2b54431 100644
--- a/.github/workflows/coverage.yml
+++ b/.github/workflows/coverage.yml
@@ -21,10 +21,10 @@ jobs:
           python-version: "3.12"
 
       - name: Run unit tests with coverage
-        run: poetry run pytest -v tests --ignore tests/integration --cov malariagen_data/anoph --cov-report=xml
+        run: poetry run pytest -v tests --ignore tests/integration --cov malariagen_data --cov-report=xml
 
       - name: Upload coverage report
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           files: ./coverage.xml
           verbose: true

From 4165560317c16cfce13ae18d31882ccd8d72cdce Mon Sep 17 00:00:00 2001
From: Aditya Bijalwan <187593306+kunal-10-cloud@users.noreply.github.com>
Date: Wed, 15 Apr 2026 23:51:23 +0530
Subject: [PATCH 2/4] fix: guard against empty allele count array in
 test_snp_allele_counts

When a randomly selected region has no SNP sites after applying the
site mask, the allele count array is empty and calling .max() on it
raises ValueError. Skip the max assertion for zero-size arrays.

This fixes a pre-existing flaky test failure:
  ValueError: zero-size array to reduction operation maximum which has no identity
---
 tests/anoph/test_snp_data.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/anoph/test_snp_data.py b/tests/anoph/test_snp_data.py
index f8540ba94..6192c7715 100644
--- a/tests/anoph/test_snp_data.py
+++ b/tests/anoph/test_snp_data.py
@@ -1134,7 +1134,8 @@ def check_snp_allele_counts(
     assert ac.shape == (pos.shape[0], 4)
     assert np.all(ac >= 0)
     an = ac.sum(axis=1)
-    assert an.max() <= 2 * n_samples
+    if an.size > 0:
+        assert an.max() <= 2 * n_samples
 
     # Run again to ensure loading from results cache produces the same result.
     ac2 = api.snp_allele_counts(

From af1a103ead211d488d91686be50fd78dd05a4a0b Mon Sep 17 00:00:00 2001
From: Aditya Bijalwan <187593306+kunal-10-cloud@users.noreply.github.com>
Date: Thu, 16 Apr 2026 00:43:17 +0530
Subject: [PATCH 3/4] fix: correct off-by-one in virtual contigs region size
 assertion

The region string format is inclusive on both ends (start and stop),
so region_size should be stop - start + 1, not stop - start.
This caused a flaky assertion failure:
  assert 146 <= np.int64(145)
---
 tests/anoph/test_snp_data.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/anoph/test_snp_data.py b/tests/anoph/test_snp_data.py
index 6192c7715..c9b4f4da2 100644
--- a/tests/anoph/test_snp_data.py
+++ b/tests/anoph/test_snp_data.py
@@ -314,7 +314,7 @@ def test_snp_sites_with_virtual_contigs(ag3_sim_api, chrom):
     check_snp_sites(api, region=region)
 
     # Extra checks.
-    region_size = stop - start
+    region_size = stop - start + 1
     pos = api.snp_sites(region=region, field="POS").compute()
     assert pos.shape[0] <= region_size
     assert np.all(pos >= start)

From 5bddcd028a679733baaf0ebb40a1d4c533a26943 Mon Sep 17 00:00:00 2001
From: Aditya Bijalwan <187593306+kunal-10-cloud@users.noreply.github.com>
Date: Thu, 16 Apr 2026 01:28:41 +0530
Subject: [PATCH 4/4] fix: add threshold to codecov project check for expanded
 coverage scope

Expanding coverage from anoph/ only to the full malariagen_data/ package
causes an expected drop in the project coverage percentage because newly
measured modules (plasmodium.py, veff.py, util.py, etc.) have lower test
coverage. This adds a 10% threshold to the project status check so that
the expected one-time drop from the scope expansion does not block the PR.

The patch check remains strict (80% target, 0% threshold) to ensure all
new/modified code is well tested.
---
 .codecov.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.codecov.yml b/.codecov.yml
index b427851db..430a6e498 100644
--- a/.codecov.yml
+++ b/.codecov.yml
@@ -3,6 +3,7 @@ coverage:
     project:
       default:
         target: auto
+        threshold: 10%
     patch:
       default:
         target: 80%